Subject: Re: CCL:Second negative frequency

From: David Turner <[email-masked]>
Date: Tue, 13 Feb 2001 09:17:20 +0100

Your second value (36 cm-1) could easily be positive given the error 
associated with normal mode calculations (+/-50 cm-1 or so). Perhaps
you have only one imaginary frequency ...

David

Ivan wrote:
> 
> Dear CCL'ers
> 
> I am working with programme GAMESS and an present time I am facing some
> problems with TS.I am simulating H-transfer from NH3 bonded to the rest of
> molecule to another "free" NH3 forming "free"NH4.
> In TS there are two imaginary frequencies ( 1. - value about 975, that
> correspond to H-transfer and 2.- value about 36 )  and  can't get rid of
> this second little negative frequency. Firstly I tried to use keywords
> PURIFY in $STATPT and $FORCE groups to purify hessian matrix but with no
> results. Then I tried several approachs to find better TS, but all resulted
> to the same TS. And IRC calculations in both directions are correct, because
> according to IRC's this TS connects appropriate minimas on both side of the
> hill.Finally I wanted to to perform IRC folowing the second negative
> frequency, but GAMESS did not accept the specified frequency ( in $IRC
> group ).
> 
> I would very appreciate any help,advice or trick.
> 
> Stanislav Ivan
> student
> 
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---

From: "Dr. Peter Burger" <[email-masked]>
Date: Tue, 13 Feb 2001 11:44:12 +0100 (CET)

Good point,

however, what are you going to do about it? I spent alot computer time
in reoptimizing using the calculated hessian / recalculating the second
derivatives (sometimes several times) and had the excact same question.
I analyzed these low frequencies and in my case quite often these were
just rotations of methyl groups etc. in the peripheral positions, while
the larger imaginary frequency was corresponding to the TS.  

Anyways, this made me wonder how this is handled
in publications. Are these sometimes small frequencies 
sometimes ignored? Will this be always mentioned
in the paper, would the referees accept additional imaginary
frequencies if they had been analyzed thoroughly?

 Sorry, for this question I do not want to
blame anyone - but being originally  not trained
as an theoretical chemist, I am just curious.  So far,
I was lucky to get rid of all additional negative frequencies, 
by reoptimization, but considering the usual error bars of these
frequencies as mentioned in the last post and the size of some of my
systems (DFT on 50-130 atoms with numerical second derivatives by finite
difference), I could be tempted to just mention in the paper that
that there is a residual small imaginary frequency, which I
cannot get rid of with reasonable computational effort, e.g. redo the
force calculation a third or forth time.

Any comments?

Peter

---

From: "Samuel A. Abrash" <[email-masked]>
Date: Tue, 13 Feb 2001 08:57:28 -0500

Of course there is the possibility that it is real.  I haven't looked at
the molecule under discussion but many molecules have internal rotation
degrees of freedom, or other degrees of freedom in which the potential
energy surface is very flat.  In those cases, it can be very difficult to
locate the minimum of the PES in that coordinate.  Another possibility is
that the symmetry that the calculation is being carried out in may be too
high to allow a true minimum to be reached.  Perhaps the symmetry needs to
be relaxed.

Best regards,
Sam Abrash

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